davi

Even low-dose ultrasound (what they use on pregnant woman) results in ultrastructural changes in brains [0], specifically at the nodes of Ranvier (the gaps between myelin along axons). See also [1] for a review.

[0] Ellisman MH, Palmer DE, André MP (1987), "Diagnostic levels of ultrasound may disrupt myelination," Experimental Neurology 98:78–92 https://pubmed.ncbi.nlm.nih.gov/3308504/

[1] Quarato, C.M.I., Lacedonia, D., Salvemini, M., Tuccari, G., Mastrodonato, G., Villani, R., Fiore, L.A., Scioscia, G., Mirijello, A., Saponara, A. and Sperandeo, M., 2023. A review on biological effects of ultrasounds: key messages for clinicians. Diagnostics, 13(5), p.855. https://pmc.ncbi.nlm.nih.gov/articles/PMC10001275/

In summer of 1997 I interned at the Santa Fe Institute. Barry McMullin was there as well, using swarm (an early cellular automata library) to reimplement and extend the original autopoiesis algorithm. His report: https://www.santafe.edu/research/results/working-papers/comp...

And a later study by him: https://pubmed.ncbi.nlm.nih.gov/15245628/

True. And this approach continues - the IARPA MICrONs program is trying to do a mm cube of mouse visual cortex: https://www.iarpa.gov/index.php/research-programs/microns

In the fruit fly, neuronal cell types are highly morphologically stereotyped and identifiable across animals. This means that for a given cell type, you can collect data on electrical synapses in animal A, on transmitters in animal B, and on electrophysiology in animal C, and in this fashion assemble a unified, multimodal view of the parts involved. Our whole brain EM volume lets you see how those parts are connected.

In the above examples dead brains are okay except for electrophysiology, where the brain needs to be alive.

Late to the party, but corresponding author on the paper here. Cool to see this on HN!

We have less than "half the picture" here. Not just weights; also missing electrical synapses, neurotransmitters, etc. We also don't know the spatial scale of neuronal arbor integration. Furthermore these are just the image data, not the complete connectome; people still have to trace circuits by hand in this dataset. Collaborators are starting to crack the segmentation problem, but it is still early days.

Necessary but insufficient class of information!

If anyone is interested you can browse the data live here:https://fafb.catmaid.virtualflybrain.org/?pid=2&zp=131280&yp...

"URL to this view" lets you share URLs to whatever you're looking at.

---- edit:

in mammals there is pretty good circumstantial evidence that post-synaptic density size correlates with evoked postsynaptic potential, but this hasn't been clearly and directly calibrated yet, and could vary from cell type to cell type

Hey cool, 3rd author Shane Gonin is now at Janelia (where my lab is) and I know a bit about this work. Funny to see it pop up here.

The kind of electron microscopy (EM) of brain tissue I do relies upon embedding the tissue in a resin called Epon. Epon has excellent cutting properties and low intrinsic contrast in EM. But in order to embed tissue in Epon it has to be completely dehydrated, which quenches genetically expressed fluorphores like GFP.

My fantasy for these genetically expressed buckyball-like proteins is that one could engineer their interior to be sufficiently hydrophilic that GFP fluorescence would survive complete dehydration of the surrounding tissue, instead relying on the polarized residues of the amino acids in the interior. This would let us combine highest quality EM with highest quality light microscopy in the same sample -- which would be very useful indeed.

"The day will come when David Bowie is a star and the crushed remains of his melodies are broadcast from Muzak boxes in every elevator and hotel lobby in town."

- Nancy Erlich, July 11 1971 New York Times (http://timesmachine.nytimes.com/timesmachine/1971/07/11/9130...)

Whups, forgot the email in my HN profile isn't visible, and now too late to edit the post; here are some links:

- website & email: https://www.janelia.org/lab/bock-lab; [email protected]

- more on our approach to electron microscopy: http://reid.med.harvard.edu/pdf/Bock-Lee-etal-Reid-2011-Natu... http://reid.med.harvard.edu/pdf/Bock-Lee-etal-Reid-2011-Natu...

Bock lab, Janelia research campus, Howard Hughes Medical Institute (HHMI) | Ashburn, VA | ONSITE

Data scientist / Neurogeometer

We recently finished acquiring an electron microscopy dataset encompassing the entire brain of a fruitfly (120 million images, 115 TB on disk, voxel size 4 x 4 x 40 nanometers). A team of tracers is manually skeletonizing portions of this animal's nervous system, and we are starting to see interesting circuit motifs emerge.

We are looking for someone to help build and use tools supporting this analysis (neurogeometry), as well as help wrangle the millions of images continuing to flow from our three microscopes (~500 TB of primary image data anticipated in the next two years). During this time we expect to switch from RAID-based file systems to an object store (likely Scality), with substantial support from a team at Janelia outside the lab.

Desirable attributes:

- Education: B.S. or M.S. in Computer Science or related field (or an equivalent in education and experience)

- Strong familiarity with Linux, including command line wizardry and detangling dependency nightmares

- Proficient in Python and at least one other programming language (e.g Java or C/C++)

- Experience with utilizing SQL and/or NoSQL data stores (e.g. MongoDB, PostgreSQL, Microsoft SQL Server)

- Experience with image processing (ImageJ, SciPy, Matlab, OpenCV, etc.)

- Comfortable working with new programming languages and tools when necessary

- Familiar with RESTful web services

- Experience using an HPC cluster (MPI, SGE/OGE, Spark, etc.)

- Follows current trends in industry and academia

- Willing to get hands dirty with hardware

- Ability to concentrate in a fast paced and dynamic environment

- Ability to communicate effectively, orally and in writing

- Ability to take initiative, prioritize tasks, use good judgement and monitor completion of assigned duties.

- Experience or strong interest in working in an interdisciplinary environment.

Classic quote: “Harald is much smarter,” Betzig said. “When I left Bell Labs, I said ‘fuck you.’ When Harald left, he took all his equipment.”

I wrote about this here five and a half years ago, before it went "sour so quickly": https://news.ycombinator.com/item?id=470181

As a grad student back then, I saw a pyramid scheme. Training programs were (and are) funding way more students than there is room at the top. If funding at the top level stops expanding, the current scenario unfolds.

If I have undergrads in my lab who want to go on to graduate school, I give them sufficient information on these numbers that they can provide "informed consent". If they still want to go ahead, they receive my full support.